17-70299100-T-G

Variant names:

• chr17-70299100-T-G
• rs312692
• ENST00000771979.1:n.146-5854T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000771979.1(ENSG00000300458):​n.146-5854T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.763 in 152,108 control chromosomes in the GnomAD database, including 44,586 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.76 (44586 hom., cov: 31)
• Consequence: ENSG00000300458 ENST00000771979.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99
• Publications: 5 publications found

Genes affected

ENSG00000300458 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300458	ENST00000771979.1	n.146-5854T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.763 AC: 115966 AN: 151990 Hom.: 44548 Cov.: 31

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.826

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.757

Gnomad OTH AF: 0.764

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.763 AC: 116054 AN: 152108 Hom.: 44586 Cov.: 31 AF XY: 0.764 AC XY: 56829 AN XY: 74350

African (AFR) AF: 0.806 AC: 33445 AN: 41474

American (AMR) AF: 0.703 AC: 10744 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2426 AN: 3472

East Asian (EAS) AF: 0.528 AC: 2727 AN: 5162

South Asian (SAS) AF: 0.827 AC: 3984 AN: 4820

European-Finnish (FIN) AF: 0.829 AC: 8771 AN: 10578

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.757 AC: 51476 AN: 68002

Other (OTH) AF: 0.764 AC: 1612 AN: 2110

Alfa AF: 0.758 Hom.: 7407

Bravo AF: 0.749

Asia WGS AF: 0.693 AC: 2411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.49
DANN	Benign	0.65
PhyloP100		-2.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs312692; hg19: chr17-68295241;